The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was established in 2002 with the aim of defining community standards for data representation in proteomics and facilitating data comparison, exchange and verification. The 2013 annual spring workshop was hosted by the University of Liverpool, UK and concentrated on updating and refining the existing standards in the light of new methodologies and technologies. To control the inflation of file sizes, strategies for file compression, particularly for mzML files, were explored. Best practices for encoding information such as protein grouping and PTM localisation were refined and documented. Additional example files for the mzQuantML format were designed to provide support for selected reaction monitoring techniques. Enhancements to the PSI Common Query Interface (PSICQUIC) and PSI-MI XML were discussed. Finally, the group engaged in discussion on how the existing work of the HUPO-PSI can be leveraged by the Metabolomics Standards Initiative to improve the capture of metabolite data.